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    LIMS1 LIM zinc finger domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 3987, updated on 3-Mar-2019

    Summary

    Official Symbol
    LIMS1provided by HGNC
    Official Full Name
    LIM zinc finger domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:6616
    See related
    Ensembl:ENSG00000169756 MIM:602567
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PINCH; PINCH1; PINCH-1
    Summary
    The protein encoded by this gene is an adaptor protein which contains five LIM domains, or double zinc fingers. The protein is likely involved in integrin signaling through its LIM domain-mediated interaction with integrin-linked kinase, found in focal adhesion plaques. It is also thought to act as a bridge linking integrin-linked kinase to NCK adaptor protein 2, which is involved in growth factor receptor kinase signaling pathways. Its localization to the periphery of spreading cells also suggests that this protein may play a role in integrin-mediated cell adhesion or spreading. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
    Expression
    Ubiquitous expression in endometrium (RPKM 18.5), adrenal (RPKM 16.0) and 25 other tissues See more
    Orthologs

    Genomic context

    See LIMS1 in Genome Data Viewer
    Location:
    2q12.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (108534355..108687246)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (109150811..109303702)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene GRIP and coiled-coil domain containing 2 Neighboring gene 2q12.3 distal recombination region Neighboring gene GCC2 antisense RNA 1 Neighboring gene LIMS1 antisense RNA 1 Neighboring gene cytochrome c oxidase subunit 7B, mitochondrial pseudogene Neighboring gene ribosomal protein L10 pseudogene 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    zinc ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    cell-cell junction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    focal adhesion HDA PubMed 
    focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with focal adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    LIM and senescent cell antigen-like-containing domain protein 1
    Names
    LIM and senescent cell antigen-like domains 1
    LIM-type zinc finger domains 1
    particularly interesting new Cys-His protein 1
    renal carcinoma antigen NY-REN-48
    senescent cell antigen

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001193482.1NP_001180411.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC010095, AF527762, AL110164
      Consensus CDS
      CCDS54383.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000386926.1, ENST00000410093.5
      Conserved Domains (5) summary
      cd09331
      Location:1472
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:75126
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:139189
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:195248
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:256309
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    2. NM_001193483.2NP_001180412.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform d

      See identical proteins and their annotated locations for NP_001180412.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (d) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC010095, AK296992, AL110164, DC401794
      Consensus CDS
      CCDS54382.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000437912.1, ENST00000544547.5
      Conserved Domains (5) summary
      cd09331
      Location:2280
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:83134
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:147197
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:203256
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:264317
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    3. NM_001193484.1NP_001180413.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform e

      See identical proteins and their annotated locations for NP_001180413.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (e) is shorter and has a distinct N-terminus, compared to isoform a.
      Source sequence(s)
      AC010095, AF527761, AK304260, AL110164
      Consensus CDS
      CCDS54384.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000387264.1, ENST00000409441.5
      Conserved Domains (5) summary
      cd09331
      Location:47105
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:108159
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:172222
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:228281
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:289342
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    4. NM_001193485.2NP_001180414.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform a

      See identical proteins and their annotated locations for NP_001180414.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC010095, AF527759, AL110164
      Consensus CDS
      CCDS54385.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000337598.4, ENST00000338045.7
      Conserved Domains (5) summary
      cd09331
      Location:72130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314367
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    5. NM_001193488.1NP_001180417.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform b

      See identical proteins and their annotated locations for NP_001180417.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AC010095, AF527763, AL110164, BC005341
      Consensus CDS
      CCDS2078.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000376987.1, ENST00000393310.5
      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    6. NM_004987.5NP_004978.2  LIM and senescent cell antigen-like-containing domain protein 1 isoform b

      See identical proteins and their annotated locations for NP_004978.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus compared to isoform a. Variants 2 and 3 both encode the same isoform (b).
      Source sequence(s)
      AC010095, AL110164, BG942518, U09284
      Consensus CDS
      CCDS2078.1
      UniProtKB/Swiss-Prot
      P48059
      Related
      ENSP00000331775.6, ENST00000332345.10
      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

      Range
      108534355..108687246
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004092.1XP_016859581.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

    2. XM_005263949.1XP_005264006.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X3

      See identical proteins and their annotated locations for XP_005264006.1

      Conserved Domains (5) summary
      cd09331
      Location:2280
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:83134
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:147197
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:203256
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:264317
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    3. XM_017004094.1XP_016859583.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

    4. XM_005263951.5XP_005264008.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

      See identical proteins and their annotated locations for XP_005264008.1

      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    5. XM_005263950.2XP_005264007.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X4

      See identical proteins and their annotated locations for XP_005264007.1

      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    6. XM_024452885.1XP_024308653.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X5

      Conserved Domains (5) summary
      cd09331
      Location:1068
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:71122
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:135185
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:191244
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:252305
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    7. XM_005263948.4XP_005264005.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X2

      See identical proteins and their annotated locations for XP_005264005.1

      Conserved Domains (5) summary
      cd09331
      Location:47105
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:108159
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:172222
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:228281
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:289342
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    8. XM_017004093.1XP_016859582.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

    9. XM_017004091.1XP_016859580.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X6

    10. XM_005263946.1XP_005264003.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X1

      Conserved Domains (5) summary
      cd09331
      Location:72130
      LIM1_PINCH; The first LIM domain of protein PINCH
      cd09332
      Location:133184
      LIM2_PINCH; The second LIM domain of protein PINCH
      cd09333
      Location:197247
      LIM3_PINCH; The third LIM domain of protein PINCH
      cd09334
      Location:253306
      LIM4_PINCH; The fourth LIM domain of protein PINCH
      cd09335
      Location:314367
      LIM5_PINCH; The fifth LIM domain of protein PINCH
    11. XM_017004095.1XP_016859584.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X7

    12. XM_017004096.1XP_016859585.1  LIM and senescent cell antigen-like-containing domain protein 1 isoform X8

      UniProtKB/TrEMBL
      F8WC86
      Related
      ENSP00000399267.2, ENST00000414829.2
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